I-H-108333

Patient I-H-108333


Individual DMP ID: P-0006237

Gender: MALE

Disease(s): UNDIFFERENTIATED SARCOMA (UNDIFS)

Part C Consent: True

Number of WGS Samples: 1

Number of RNAseq Samples: 1

CBio Portal Results:


Tumor_Sample_Barcode Chromosome Start_Position Reference_Allele Tumor_Seq_Allele2 Hugo_Symbol VAF Variant_Classification HGVSp_Short
P-0006237-T04-IM6 3 178917478 G A PIK3CA 0.270423 Missense_Mutation p.G118D

          

RNA Sample: I-H-108333-T2-1-R1-1

Disease: UNDIFFERENTIATED SARCOMA (UNDIFS)

Tissue Site: R Gluteal Mass

Days since birth at collection: 8029


          

Fusion Results:


High Confidence Fusions:

GENE1 GENE2 DESCRIPTION SPAN_READS SPLIT_READS LEFTBREAK RIGHTBREAK CALLER_EFFECT ANNOT_EFFECT CALLER NUM_CALLERS
MGA NUTM1 oncogene,cancer,exon-exon 14 19 15:42054560:+ 15:34640170:+ in-frame in-frame FUSIONCATCHER 3


          

Expression TSNE Results:


Bokeh Application

          

Overexpressed Cancer Genes:


Gene Log Fold Change Loc Cancers
NUTM1 7.61806 15q14 lethal midline carcinoma
OLIG2 4.29052 21q22.11 T-ALL
MLF1 3.65278 3q25.1 AML
LRIG3 2.29114 12q14.1 NSCLC
SFRP4 2.16084 7p14.1 colorectal cancer, melanoma, SCC, gastric cancer, oesophageal SCC

          

WGS Sample: I-H-108333-T2-2-D1-1

Disease: UNDIFFERENTIATED SARCOMA (UNDIFS)

Tissue Site: R Gluteal Mass

Days since birth at collection: 8029

Normal used: I-H-108333-N2-1-D1-1

Median Coverage: 115

MSISensor HAS NOT BEEN RUN


          

Copy Number Results:


Tumor Purity: 0.9

Tumor Ploidy: 2.24

No Amplifications or Homozygous losses for Oncogenes or TSGs

SNV Results:


SNV Likely Drivers:

CHR START GENE EFFECT cDNA_CHANGE PROTEIN_CHANGE TARGET_VAF REFERENCE_VAF REFERENCE_DEPTH Oncogene TSG CCF GENE_TPM
3 178917478 PIK3CA non_synonymous_codon c.353G>A p.G118D 0.35 0 37 0.785316 9.70179

Indel Results:


Indel Likely Drivers:

No Indel Likely Drivers

Rearrangement Results:


Rearranged Tumor Suppressor Genes:

gene1 gene2 svclass brass_score
EPHB2 BACH2 translocation 45
AGAP1 HDAC4 inversion 43
_ HDAC4 inversion 29
_ NF2 translocation 43
TERT TERT deletion 5

Rearranged Oncogenes:

gene1 gene2 svclass brass_score
AGAP1 HDAC4 inversion 43
_ HDAC4 inversion 29
TERT TERT deletion 5
COL4A3BP ROS1 translocation 37
KSR2 KSR2 tandem-duplication 46

Calls by Numbers:


SNVS Coding SNVS INDELS Coding INDELS #Coding/Mb #Muts/Mb REARR
I-H-108333-T2-2-D1-1 3575 44 490 3 1.57 1.40 61

Integrated Circos:


Mutational Signatures



END REPORT


I-H-108333

Patient I-H-108333


Individual DMP ID: P-0006237

Gender: MALE

Disease(s): UNDIFFERENTIATED SARCOMA (UNDIFS)

Part C Consent: True

Number of WGS Samples: 1

Number of RNAseq Samples: 1

CBio Portal Results:


Tumor_Sample_Barcode Chromosome Start_Position Reference_Allele Tumor_Seq_Allele2 Hugo_Symbol VAF Variant_Classification HGVSp_Short
P-0006237-T04-IM6 3 178917478 G A PIK3CA 0.270423 Missense_Mutation p.G118D

          

RNA Sample: I-H-108333-T2-1-R1-1

Disease: UNDIFFERENTIATED SARCOMA (UNDIFS)

Tissue Site: R Gluteal Mass

Days since birth at collection: 8029


          

Fusion Results:


High Confidence Fusions:

GENE1 GENE2 DESCRIPTION SPAN_READS SPLIT_READS LEFTBREAK RIGHTBREAK CALLER_EFFECT ANNOT_EFFECT CALLER NUM_CALLERS
MGA NUTM1 oncogene,cancer,exon-exon 14 19 15:42054560:+ 15:34640170:+ in-frame in-frame FUSIONCATCHER 3


          

Expression TSNE Results:


Bokeh Application

          

Overexpressed Cancer Genes:


Gene Log Fold Change Loc Cancers
NUTM1 7.61806 15q14 lethal midline carcinoma
OLIG2 4.29052 21q22.11 T-ALL
MLF1 3.65278 3q25.1 AML
LRIG3 2.29114 12q14.1 NSCLC
SFRP4 2.16084 7p14.1 colorectal cancer, melanoma, SCC, gastric cancer, oesophageal SCC

          

WGS Sample: I-H-108333-T2-2-D1-1

Disease: UNDIFFERENTIATED SARCOMA (UNDIFS)

Tissue Site: R Gluteal Mass

Days since birth at collection: 8029

Normal used: I-H-108333-N2-1-D1-1

Median Coverage: 115

MSISensor HAS NOT BEEN RUN


          

Copy Number Results:


Tumor Purity: 0.9

Tumor Ploidy: 2.24

No Amplifications or Homozygous losses for Oncogenes or TSGs

SNV Results:


SNV Likely Drivers:

CHR START GENE EFFECT cDNA_CHANGE PROTEIN_CHANGE TARGET_VAF REFERENCE_VAF REFERENCE_DEPTH Oncogene TSG CCF GENE_TPM
3 178917478 PIK3CA non_synonymous_codon c.353G>A p.G118D 0.35 0 37 0.785316 9.70179

Indel Results:


Indel Likely Drivers:

No Indel Likely Drivers

Rearrangement Results:


Rearranged Tumor Suppressor Genes:

gene1 gene2 svclass brass_score
EPHB2 BACH2 translocation 45
AGAP1 HDAC4 inversion 43
_ HDAC4 inversion 29
_ NF2 translocation 43
TERT TERT deletion 5

Rearranged Oncogenes:

gene1 gene2 svclass brass_score
AGAP1 HDAC4 inversion 43
_ HDAC4 inversion 29
TERT TERT deletion 5
COL4A3BP ROS1 translocation 37
KSR2 KSR2 tandem-duplication 46

Calls by Numbers:


SNVS Coding SNVS INDELS Coding INDELS #Coding/Mb #Muts/Mb REARR
I-H-108333-T2-2-D1-1 3575 44 490 3 1.57 1.40 61

Integrated Circos:


Mutational Signatures



END REPORT